Summary information

PDB id
8fhx
Class
DNA
Method
X-ray (2.5 Å)
Summary
Structure of lettuce aptamer bound to dfhbi-1t
Reference
Passalacqua LFM, Banco MT, Moon JD, Li X, Jaffrey SR, Ferre-D'Amare AR (2023): "Intricate 3D architecture of a DNA mimic of GFP." Nature, 618, 1078-1084. doi: 10.1038/s41586-023-06229-8.
Abstract
Numerous studies have shown how RNA molecules can adopt elaborate three-dimensional (3D) architectures1-3. By contrast, whether DNA can self-assemble into complex 3D folds capable of sophisticated biochemistry, independent of protein or RNA partners, has remained mysterious. Lettuce is an in vitro-evolved DNA molecule that binds and activates4 conditional fluorophores derived from GFP. To extend previous structural studies5,6 of fluorogenic RNAs, GFP and other fluorescent proteins7 to DNA, we characterize Lettuce-fluorophore complexes by X-ray crystallography and cryogenic electron microscopy. The results reveal that the 53-nucleotide DNA adopts a four-way junction (4WJ) fold. Instead of the canonical L-shaped or H-shaped structures commonly seen8 in 4WJ RNAs, the four stems of Lettuce form two coaxial stacks that pack co-linearly to form a central G-quadruplex in which the fluorophore binds. This fold is stabilized by stacking, extensive nucleobase hydrogen bonding-including through unusual diagonally stacked bases that bridge successive tiers of the main coaxial stacks of the DNA-and coordination of monovalent and divalent cations. Overall, the structure is more compact than many RNAs of comparable size. Lettuce demonstrates how DNA can form elaborate 3D structures without using RNA-like tertiary interactions and suggests that new principles of nucleic acid organization will be forthcoming from the analysis of complex DNAs.
G4 notes
2 G-tetrads, 1 G4 helix, 1 G4 stem, 2(+Ln+Lw+Ln), chair(2+2), UDUD

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 2 G-tetrads

 1 glyco-bond=s-s- sugar=.--- groove=wnwn planarity=0.587 type=other  nts=4 GGGG A.DG9,A.DG46,A.DG24,A.DG19
 2 glyco-bond=-s-s sugar=---. groove=wnwn planarity=0.534 type=bowl-2 nts=4 GGGG A.DG10,A.DG45,A.DG25,A.DG18

List of 1 G4-helix

In DSSR, a G4-helix is defined by stacking interactions of G-tetrads, regardless of backbone connectivity, and may contain more than one G4-stem.

Helix#1, 2 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=s-s- sugar=.--- groove=wnwn Major-->WC nts=4 GGGG A.DG9,A.DG46,A.DG24,A.DG19
 2  glyco-bond=-s-s sugar=---. groove=wnwn WC-->Major nts=4 GGGG A.DG10,A.DG45,A.DG25,A.DG18
  step#1  mm(<>,outward)  area=19.86 rise=3.55 twist=14.1
  strand#1 DNA glyco-bond=s- sugar=.- nts=2 GG A.DG9,A.DG10
  strand#2 DNA glyco-bond=-s sugar=-- nts=2 GG A.DG46,A.DG45
  strand#3 DNA glyco-bond=s- sugar=-- nts=2 GG A.DG24,A.DG25
  strand#4 DNA glyco-bond=-s sugar=-. nts=2 GG A.DG19,A.DG18

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1 stacking diagram 
 1  glyco-bond=s-s- sugar=.--- groove=wnwn Major-->WC nts=4 GGGG A.DG9,A.DG46,A.DG24,A.DG19
 2  glyco-bond=-s-s sugar=---. groove=wnwn WC-->Major nts=4 GGGG A.DG10,A.DG45,A.DG25,A.DG18
  step#1  mm(<>,outward)  area=19.86 rise=3.55 twist=14.1

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List of 1 G4-stem

In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands.

Stem#1, 2 G-tetrad layers, 3 loops, INTRA-molecular, UDUD, anti-parallel, 2(+Ln+Lw+Ln), chair(2+2)

 1  glyco-bond=s-s- sugar=.--- groove=wnwn Major-->WC nts=4 GGGG A.DG9,A.DG46,A.DG24,A.DG19
 2  glyco-bond=-s-s sugar=---. groove=wnwn WC-->Major nts=4 GGGG A.DG10,A.DG45,A.DG25,A.DG18
  step#1  mm(<>,outward)  area=19.86 rise=3.55 twist=14.1
  strand#1  U DNA glyco-bond=s- sugar=.- nts=2 GG A.DG9,A.DG10
  strand#2  D DNA glyco-bond=-s sugar=-- nts=2 GG A.DG46,A.DG45
  strand#3  U DNA glyco-bond=s- sugar=-- nts=2 GG A.DG24,A.DG25
  strand#4  D DNA glyco-bond=-s sugar=-. nts=2 GG A.DG19,A.DG18
  loop#1 type=lateral   strands=[#1,#4] nts=7 ATGATGC A.DA11,A.DT12,A.DG13,A.DA14,A.DT15,A.DG16,A.DC17
  loop#2 type=lateral   strands=[#4,#3] nts=4 CAGT A.DC20,A.DA21,A.DG22,A.DT23
  loop#3 type=lateral   strands=[#3,#2] nts=19 GCTTCGCAGTTCCTGCGAG A.DG26,A.DC27,A.DT28,A.DT29,A.DC30,A.DG31,A.DC32,A.DA33,A.DG34,A.DT35,A.DT36,A.DC37,A.DC38,A.DT39,A.DG40,A.DC41,A.DG42,A.DA43,A.DG44

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